SynBERC:COG

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Welcome to the Construction Optimization Group (COG)!

At the last SynBERC retreat SynBERCers decided that solving the challenge of automated DNA assembly/cloning would be a priority for the center. COG will be tasked with drafting a report for the upcoming NSF visit in March(?) that evaluates current assembly approaches and proposes a path forward. This page is just getting started, please add/edit!

Goals

  1. Maintain communication across labs on status of automated assembly projects.
  2. Produce a report with evaluation of current assembly approaches and recommendations for going forward.

COG:Meeting 1

Agenda:

What are the goals for COG?

Proposed based on SynBERC meeting / conversations since:

  1. Stay up to date with current automated cloning research projects taking place in SynBERC labs
  2. Get the ball rolling for solving the automated cloning problem in the short term

Research Updates

  • 1/2 the meeting?
  • Brief updates from each of the groups? one longer presentation each month about one project?
    • Something else?

Getting the ball rolling for solving automated cloning

  1. Define the problem we want solved
  2. Specify the possible solutions
  3. Evaluate / Act on solutions

Define problem

  • Combinatorial libraries of assembled parts (Wendall, UCSF iGEM team project)
  • Automation of standard BioBrick Assembly (Registry)
  • Automation of assembly independent of BBs (Synth companies?)

Specify Possible Solutions

  1. Decentralized approach
    • We make cloning easier by using some automation combined with "normal" individual cloning approaches. For example, each lab buys a Qiacube to partially automate minipreps and restriction digests. Then ligations and transformations are done by hand at the bench.
  2. Centralized academic facility
    • We find the resources to start an assembly facility similar to how sequencing facilities are set up on campus
  3. Outsource to DNA synthesis company
    • We work with a DNA synthesis company so that they can offer commercial automated cloning services. How do we ensure that such a partnership wouldn't fall apart as soon as a big synthesis order comes along? Automated cloning may be too small a market and/or too large a problem for DNA synthesis companies to tackle right now?

Evaluate / Act on Solutions

  • Registry hires more staff to do process engineering
  • Trial QIAcube / other "cheap" robots for distributed approach
  • Figure out how big an assembly order iGEM + labs using parts could put together for a Synth company (George suggestion)
  • Go talk to Synth companies see if they'll do this.
  • Plot the cost of synth vs. assembly over time for particular length scales (drew's suggestion)

Meeting Frequency

  • Monthly?
  • Any weekday's particularly bad for certain groups? (Weds at MIT)

Next steps

Communication

Members

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